This is based up upon comic cannon along with a few silly headcanon things of mine that were made back when I had only seen X2: X-Men United, like first semester of junior year. Jeez, I've procrastinated WAY too much. (I'm a senior now for prospective.)
Eleanor 'Ellie' Magda Frost is not bionic. She has powers but she is not bionic. She has telepathic and magnetic powers. Nobody has bionic powers that are similar to hers, not even Krane or his Bionic Super Soldiers. Ellie was unique. She was unique not just in her powers but in her personality. She was the only one who laughed at his jokes, let alone understood them. He was in love with her. Sebastian Cole Krane was in love with Eleanor Magda Frost.
Eleanor 'Ellie' Magda Frost was not bionic because she was a mutant. She was the daughter of Magneto, or Erik Lehnsherr, and Emma Frost. She had inherited both sets of her parent's powers, as she was an alpha mutant. She was an alpha mutant because she had two mutated X Chromosomes. It was rare for second generation mutants to have the same powers as their parents, but it could still happen. A good example was how the son of Mystique, Nightcrawler aka Kurt Wagner inherited her shapeshifting in the form of being able to camouflage. Eleanor 'Ellie' Magda Frost was special. She had always had been.
Eleanor 'Ellie' Magda Frost was strong. She didn't have Super Strength, but she was strong. She didn't have super strength, but she was strong. Her middle name, Magda, was her deceased half-sister's name. She didn't know how her first name was chosen, but Eleanor means 'Shining Light' or 'The Bright One'. She was strong, that's why he was in love with her. She was strong because like him, she had gotten the worse end of it. Krane was her kidnapper and his creator. He had used the Triton app on both of them. Krane had figured out how to control anyone with the Triton app, even if they weren't bionic. So he had kidnapped Ellie, knowing that she was a mutant. She was the only one that he kidnapped that he didn't give any bionics too. Krane had experience with mutants because of the daughter he had with Lady Deathstrike, Lillith, who was a bionic mutant. Lillith only had one parent who was a mutant, unlike Ellie. Lillith had both Lady Deathstrike's abilities and Krane's bionics.
Stronger, smarter, and faster. That was what the bionics were supposed to be. Sebastian knew that he was smarter and faster, but he didn't feel stronger. Krane had given his bionic super soldiers a bunch of abilities, and because of how he had them under the triton app, they didn't know what half of them were. Krane had wanted to take over the world with bionics. He had implanted himself with bionics while he was partnered with Douglas Davenport. Krane was partnered with Douglas because because Douglas needed money for his plan of getting Adam, Bree and Chase back. Douglas was their creator. He had genetically engineered them from scratch just like Krane had done with half of his soldiers; the other half he had kidnapped and made bionic.
The only reason that knew that Ellie was a mutant and who her parents were is because she had gotten a letter from professor Charles Xavier, a telepathic mutant who ran Xavier's School for Higher Learning and ran the X-Men. He had been friends with Magneto back in the day. Of course, they weren't friends anymore because Magneto had turned to the dark side. Because of the villains that were mutants, even with the mutant heroes, people still thought that mutants were bad, just because they were different. The same thing has happened, and was still happening with the bionics. It wasn't their fault that they were different, whether bionic or mutant. Bionics weren't illegal. They were brand new technology, but they weren't illegal.
Eleanor 'Ellie' Magda Frost was not faster or smarter, not stronger than a normal human, but she was amazing. More than Spiderman amazing. That was why Sebastian loved her. She was the love of his life. He couldn't live without her. If she died, he would kill himself. And he knew that she would do the same if he died. They were meant to be, no matter what anyone else said.
Sebastian hated Krane, but without him, he wouldn't have met her. And if he hadn't met her, then something worse than being kidnapped could happened, plus he would have never been 'born', much less created. Krane was responsible for getting the soulmates to meet, but he was also responsible for keeping them apart. He kept the boys and the girls separate as much as possible, especially when they were off the Triton app. Krane did what he needed to do in order to do what he wanted to do. He had limited memories of Ellie, all he got were flashes of her face and that blonde hair, but even before now, with him seeing her everyday, he knew that it was love. That was why he told her as soon as he was able too.
Sebastian knew that he had to protect Ellie. It wasn't that she couldn't protect herself, no; it was that he had to make sure that nothing bad happened to her. She was still learning how to use all of her powers, after all. Mutants had to learn how to use and master their powers, not just how to activate them and prevent glitches. It was even harder for Ellie because she was kidnapped away from her birth parents at a young age, not to mention how many powers she had. She needed to know how to use them so that she could fight. Because of that, she needed to go to Xavier's School of Higher Learning. Ellie had to learn how to control her powers.
Sebastian would miss her while she was gone, but it was for the best. After all, they couldn't have a mutant who didn't know how to use her powers. Plus, Ellie would still be able to visit during breaks from school. She also needed to at least meet her mother. Magneto was a different story than Emma Frost. They didn't know how he would react to Ellie. They didn't even know if he knew about her.
Ellie was strong because she had endured a lot more torture than Sebastian had. Not only that, but she had basically acted as the den mother, and had taken care of everyone, especially the younger kids. Krane had had at least 200 soldiers, whether they were kidnapped or created. Krane had learned from Douglas how to genetically engineer people. By 'learned', he had secretly been reading the research notes from when Douglas created Adam, Bree, and Chase. Krane also built his own chips. When he built them, he built them in bulk so that he could give his creations and abductees bionics quickly.
Sebastian was in love with Ellie and she was in love with him. Neither of them could live without each other and they had a future together.
I have way too many headcanons, and if Lab Rats wasn't on a channel that was a subsidy of Disney Channel, Krane's violence would be WAY, WAY worse, and everyone knows it.